Silicon-rhodamine-enabled identification for near-infrared light controlled proximity labeling in vitro and in vivo

Wenjing Wang, Hongyang Guo, Xiaosa Yan, Xuanzhen Pan, Xiaofei Wang, Yiming Rong, Zexiao Bai, Liwan Zhang, Zhaofa Wu, Xinyu Zhao, Weiren Huang, Wei Qin () and Ling Chu ()
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Wenjing Wang: Chinese Academy of Medical Sciences & Peking Union Medical College
Hongyang Guo: Tsinghua University
Xiaosa Yan: Shenzhen University Medical School
Xuanzhen Pan: Tsinghua University
Xiaofei Wang: Chinese Academy of Sciences
Yiming Rong: Tsinghua University
Zexiao Bai: Chinese Academy of Sciences
Liwan Zhang: Chinese Academy of Sciences
Zhaofa Wu: Chinese Academy of Sciences
Xinyu Zhao: Tsinghua University
Weiren Huang: the First Affiliated Hospital of Shenzhen University
Wei Qin: Tsinghua University
Ling Chu: Tsinghua University

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Advancement in fluorescence imaging techniques enables the study of protein dynamics and localization with unprecedented spatiotemporal resolution. However, current imaging tools are unable to elucidate dynamic protein interactomes underlying imaging observations. Conversely, proteomics tools such as proximity labeling enable the analysis of protein interactomes at a single time point but lack information about protein dynamics. We herein develop Silicon-rhodamine-enabled Identification (SeeID) for near-infrared light controlled proximity labeling that could bridge the gap between imaging and proximity labeling. SeeID is benchmarked through characterization of various organelle-specific proteomes and the KRAS protein interactome. The fluorogenic nature of SiR allows for intracellular proximity labeling with high subcellular specificity. Leveraging SiR as both a fluorophore and a photocatalyst, we develop a protocol that allows the study of dynamic protein interactomes of Parkin during mitophagy. We discover the association of the proteasome complex with Parkin at early time points, indicating the involvement of the ubiquitin-proteasome system for protein degradation in the early phase of mitophagy. Additionally, by virtue of the deep tissue penetration of near-infrared light, we achieve spatiotemporally controlled proximity labeling in vivo across the mouse brain cortex with a labeling depth of ~2 mm using an off-the-shelf 660 nm LED light set-up.

Date: 2025
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DOI: 10.1038/s41467-025-63496-x

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